Hi Ali,
In addition to the excellent advice from Martyn and Paul, I would suggest that you make 100% sure that you are in the right spot - if your map is in a large P1 cell and you don't have a model, it can sometimes be hard to find where your density ought to be (as the default view will be centered on the origin).
I use the following function (attached to a menu item) as a shortcut to go to the center of the scrollable map:
def goto_center_of_map():
if (scroll_wheel_map()==-1):
info_dialog("You need a map!")
else:
mol_id=scroll_wheel_map()
a=float(cell(mol_id)[0])
b=float(cell(mol_id)[1])
c=float(cell(mol_id)[2])
x=a*0.5
y=b*0.5
z=c*0.5
set_rotation_centre(x,y,z)
(The rest of my custom bits and pieces are here: https://www.dropbox.com/s/0b4bebwxw0p9x0e/oli_custom.py?dl=0)
Cheers,
Oli
On Wed, 22 Jun 2016 21:24:37 +0100, Ali Khan <[log in to unmask]> wrote:
>Hi,
>
>I am trying to view a mtz file in coot which was created from a cryoEM .mrc file. When I load the map as an .mrc file into coot, it looks fine, but when I convert this mrc file to mtz using either mrc2mtz (from https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/em_fitting/em_fitting.html) or using phenix.map_to_structure_factors, I do not see any density when this file is opened in coot0.83 using the Open MTZ option. Please advise.
>Thanks for your help!
>
>Sincerely,
>Ali Khan
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